Effect of initial inoculum on the temporal and spatial dynamics of wheat blast under field conditions in Bolivia.

Epidemiological studies to better understand wheat blast (WB) spatial and temporal patterns were conducted in three field environments in Bolivia between 2019 and 2020. The temporal dynamics of wheat leaf blast (WLB) and spike blast (WSB) were best described by the logistic model compared to the Gompertz and exponential models. The non-linear logistic infection rates (rL) were higher under defined inoculation in experiments two and three than under undefined inoculation in experiment one, and they were also higher for WSB than for WLB. The onset of WLB began with a spatial cluster pattern according to autocorrelation analysis and Moran's Index (I) values, with higher severity and earlier onset for defined than for undefined inoculation until the last sampling time. The WSB onset did not start with a spatial cluster pattern; instead, it was detected later until the last sampling date across experiments, with higher severity and earlier onset for defined than for undefined inoculation. Maximum severity (Kmax) was 1.0 for WSB, and less than 1.0 for WLB. Aggregation of WLB and WSB was higher for defined than for undefined inoculation. The directionality of hotspot development was similar for both WLB and WSB, mainly occurring concentrically for defined inoculation. Our results show no evidence of synchronized development but suggest a temporal and spatial progression of disease symptoms on wheat leaves and spikes. Thus, we recommend that monitoring and management of WB should be considered during early growth stages of wheat planted in areas of high risk.

Reconstructing the global migration history of Phytophthora infestans towards Colombia.

The evolution of new variants of plant pathogens is one of the biggest challenges to controlling and managing plant diseases. Of the forces driving these evolutionary processes, global migration events are particularly important for widely distributed diseases such as the potato late blight, caused by the oomycete Phytophthora infestans (Mont.) de Bary. However, little is known about its migration routes outside North America and Europe. This work used genotypic data from population studies to elucidate the migration history originating the Colombian P. infestans population. For this purpose, a dataset of 1706 P. infestans genotypes was recollected, representing North and South America, Europe, and Asia. Descriptive analysis and historical records from North America and Europe were used to propose three global migration hypotheses, differing on the origin of the disease (Mexico or Peru) and the hypothesis that it came back to South America from Europe. These scenarios were tested using Approximate Bayesian Computation. According to this analysis, the most probable scenario (posterior probability = 0.631) was the one proposing a Peruvian origin for P. infestans, an initial migration towards Colombia and Mexico, and a later event from Mexico to the United States, and then to Europe and Asia, with no return to northern South America. In Colombia, the scenario considering a single migration from Peru and posterior migrations within Colombia was the most probable with a posterior probability of 0.640. The obtained results support the hypothesis of a Peruvian origin for P. infestans followed by rare colonization events worldwide.

Understanding the temporal dynamics of invasive late blight populations in India for improved management practices.

The microbial oomycete pathogen, Phytophthora infestans causes severe epidemics of potato late blight in crops globally. Disease management benefits from an understanding of the diversity of pathogen populations. In this study, we explore the dynamics of P. infestans populations in the late blight-potato agro-ecosystem across the Indian subcontinent. Investigations of the macroecological observations at the field level and microbial ecological principles provided insights into future pathogen behaviour. We use a comprehensive simple sequence repeat allele dataset to demonstrate that an invasive clonal lineage called EU_13_A2 has dominated populations over 14 years across India, Bangladesh, and Pakistan. Increasing levels of sub-clonal variation were tracked over time and space and, for the first time, populations in Asia were also compared to the source populations from Europe. Within India, a regional pathogen population structure was observed with evidence for local migration, cross-border movement between surrounding countries, and introductions via imports. There was also evidence of genetic drift and between-season transmission of more strongly pathogenic sub-clones with a complete displacement of some sub-clonal types. The limited introduction of novel genotypes and the use of resistant potato cultivars could contribute to the dominance of the 13_A2 lineage. The insights will contribute to the management of the pathogen in these key global potato production regions.

Phenotypic and genetic diversity of xanthomonads isolated from pepper (Capsicum spp.) in Taiwan from 1989 to 2019.

Bacterial spot caused by Xanthomonas spp. is an economically important disease of pepper causing significant yield losses in Taiwan. Monitoring the pathogen population on a continuous basis is necessary for developing disease management strategies. We analyzed a collection of xanthomonad strains isolated from pepper in Taiwan between 1989 and 2019. Among the sequenced genomes, sixty-five were identified as Xanthomonas euvesicatoria and ten were X. perforans. Thirty-five X. euvesicatoria and ten X. perforans strains were copper tolerant, whereas only five X. euvesicatoria and none of the X. perforans strains were tolerant to streptomycin. Nine X. euvesicatoria strains were amylolytic, which is considered an unusual characteristic for X. euvesicatoria. Bayesian analysis of the population structure based on core gene SNPs clustered the strains into five clusters for X. euvesicatoria and three clusters for X. perforans. One X. perforans cluster, designated as TP-2019, appears to be a novel genetic cluster based on core genes, accessory gene content, and effector profile. This knowledge of pathogen diversity with whole genomic information will be useful in future comparative studies and in improving breeding programs to develop disease-resistant cultivars and other disease management options.

Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A Streptococcus population.

Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as "pilin types." Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies.IMPORTANCEPrecision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends.

Xanthomonas strains isolated from hosts in the Araceae reveal diverse phylogenetic relationships and origins.

The Araceae family, comprising ornamentals including Anthurium, Dieffenbachia, Philodendron, Colocasia, and Zantedeschia, is susceptible to Xanthomonas pathogens. Previous analyses have established heterogeneity in aroid strains, yet unresolved taxonomic positions and dynamics between Xanthomonas and frequently associated Stenotrophomonas in aroids necessitate in-depth genetic investigation to resolve these complex relationships. This study utilized multi-locus sequence analysis (MLSA) of housekeeping genes atpD, dnaA, dnaK, gltA, and gyrB to investigate 59 aroid strains, selected based on hosts, time, and geographical origins. After adding sequences from additional strains from NCBI GenBank, analysis of 161 concatenated sequences indicated that all aroid strains fell within Xanthomonas and Stenotrophomonas. Thirty-six strains isolated from Anthurium grouped under X. phaseoli, with outliers including one strain each in X. arboricola and X. sacchari, and two in Stenotrophomonas. Six strains from Caladium, Dieffenbachia, and Philodendron formed host-specific subgroups within X. euvesicatoria. One strain from Dieffenbachia aligned with X. campestris, while strains from Colocasia, Aglaonema, and Spathiphyllum clustered with X. sacchari. Apart from the zantedeschia strain described as X. arboricola pv. zantedeschiae, two colocasia, one epipremnum, and one anthurium strain joined the X. arboricola group. Overall, this study revealed significant heterogeneity among aroid strains, with anthurium strains clustering closely despite distant geographical origins. The analysis underscores the complexity of host-pathogen specificity within Xanthomonas and emphasizes the need for further taxonomic clarification through whole genome analysis of representative strains. The finding of this research will facilitate strain selection for inclusivity and exclusivity panels in developing diagnostic assays for X. phaseoli and xanthomonads affecting aroids.

The Tradeoffs Between Persistence and Mutation Rates at Sub-Inhibitory Antibiotic Concentrations in Staphylococcus aureus.

The rational design of the antibiotic treatment of bacterial infections employs these drugs to reach concentrations that exceed the minimum needed to prevent the replication of the target bacteria. However, within a treated patient, spatial and physiological heterogeneity promotes antibiotic gradients such that the concentration of antibiotics at specific sites is below the minimum needed to inhibit bacterial growth. Here, we investigate the effects of sub-inhibitory antibiotic concentrations on three parameters central to bacterial infection and the success of antibiotic treatment, using in vitro experiments with Staphylococcus aureus and mathematical-computer simulation models. Our results, using drugs of six different classes, demonstrate that exposure to sub-inhibitory antibiotic concentrations not only alters the dynamics of bacterial growth but also increases the mutation rate to antibiotic resistance and decreases the rate of production of persister cells thereby reducing the persistence level. Understanding this trade-off between mutation rates and persistence levels resulting from sub-inhibitory antibiotic exposure is crucial for optimizing, and mitigating the failure of, antibiotic therapy.

The dynamics of heroin and illicit opioid use disorder, casual use, treatment, and recovery: A mathematical modeling analysis.

A leading crisis in the United States is the opioid use disorder (OUD) epidemic. Opioid overdose deaths have been increasing, with over 100,000 deaths due to overdose from April 2020 to April 2021. This paper presents a mathematical model to address illicit OUD (IOUD), initiation, casual use, treatment, relapse, recovery, and opioid overdose deaths within an epidemiological framework. Within this model, individuals remain in the recovery class unless they relapse back to use and due to the limited availability of specialty treatment facilities for individuals with OUD, a saturation treatment function was incorporated. Additionally, a casual user class and its corresponding specialty treatment class were incorporated. We use both heroin and all-illicit opioids datasets to find parameter estimates for our models. Bistability of equilibrium solutions was found for realistic parameter values for the heroin-only dataset. This result implies that it would be beneficial to increase the availability of treatment. An alarming effect was discovered about the high overdose death rate: by 2046, the disorder-free equilibrium would be the only stable equilibrium. This consequence is concerning because it means the epidemic would end due to high overdose death rates. The IOUD model with a casual user class, its sensitivity results, and the comparison of parameters for both datasets, showed the importance of not overlooking the influence that casual users have in driving the all-illicit opioid epidemic. Casual users stay in the casual user class longer and are not going to treatment as quickly as the users of the heroin epidemic. Another result was that the users of the all-illicit opioids were going to the recovered class by means other than specialty treatment. However, the change in the relapse rate has more of an influence for those individuals than in the heroin-only epidemic. The results above from analyzing this model may inform health and policy officials, leading to more effective treatment options and prevention efforts.

Diversity of Genetic and Vegetative Compatibility Group of Colletotrichum coccodes Isolates from Chile Using Amplified Fragment Length Polymorphism Markers.

Colletotrichum coccodes (Wallr.) Hughes is an asexual fungus with five vegetative compatibility groups. It was postulated that C. coccodes was isolated at the center of origin of potato at one time, and due to the movement of potato around the globe, the fungus was established on each continent but became bottlenecked and genetically unable to form stable heterokaryons via vegetative compatibility grouping (VCG) studies. The objectives of this study were (i) to determine if the VCGs around the world are related to the VCGs in Chile, (ii) to determine the diversity of C. coccodes populations in Chile, and (iii) to find any evidence for a cryptic sexual life cycle for this fungus. Worldwide C. coccodes populations have been found to be genetically correlated and belong to one or more C. coccodes-identified VCGs. The most distributed VCG in Chile was VCG2, which is the most common VCG in North America. We hypothesize that one or more VCGs had spread from Chile to the rest of the world. Precautions and further studies should be investigated by using other molecular markers and gene sequencing.

Surviving the serenade: how conflicting selection pressures shape the early stages of sexual signal diversification.

Understanding how the early stages of sexual signal diversification proceed is critically important because these microevolutionary dynamics directly shape species trajectories and impact macroevolutionary patterns. Unfortunately, studying this is challenging because signals involve complex interactions between behavior, morphology, and physiology, much of which can only be measured in real-time. In Hawaii, male Pacific field cricket song attracts both females and a deadly parasitoid fly. Over the past two decades, there has been a marked increase in signal variation in Hawaiian populations of these crickets, including novel male morphs with distinct mating songs. We capitalize on this rare opportunity to track changes in morph composition over time in a population with three novel morphs, investigating how mate and parasitoid attraction (components of sexual and natural selection) may shape signal evolution. We find dramatic fluctuation in morph proportions over the three years of the study, including the arrival and rapid increase of one novel morph. Natural and sexual selection pressures act differently among morphs, with some more attractive to mates and others more protected from parasitism. Collectively, our results suggest that differential protection from parasitism among morphs, rather than mate attraction, aligns with recent patterns of phenotypic change in the wild.

Large-scale genotypic identification reveals density-dependent natal dispersal patterns in an elusive bird of prey.

BACKGROUND: Natal dispersal, the distance between site of birth and site of first breeding, has a fundamental role in population dynamics and species' responses to environmental changes. Population density is considered a key driver of natal dispersal. However, few studies have been able to examine densities at both the natal and the settlement site, which is critical for understanding the role of density in dispersal. Additionally, the role of density on natal dispersal remains poorly understood in long-lived and slowly reproducing species, due to their prolonged dispersal periods and often elusive nature. We studied the natal dispersal of the white-tailed eagle (Haliaeetus albicilla) in response to local breeder densities. We investigated the effects of the number of active territories around the natal site on (a) natal dispersal distance and (b) the difference between natal and settlement site breeder density. We were interested in whether eagles showed tendencies of conspecific attraction (positive density-dependence) or intraspecific competition (negative density-dependence) and how this related to settlement site breeder density. METHODS: We used a combination of long-term visual and genotypic identification to match individuals from their breeding site to their natal nest. We identified natal dispersal events for 355 individuals hatched between 1984 and 2015 in the Baltic Sea coast and Arctic areas of Finland. Of those, 251 were identified by their genotype. RESULTS: Individuals born in high-density areas dispersed shorter distances than those born in low-density areas, but settled at lower density breeding sites in comparison to their natal site. Eagles born in low natal area densities dispersed farther but settled in higher density breeding sites compared to their natal site. CONCLUSIONS: We show that eagles might be attracted by conspecifics (positive density-dependence) to identify high-quality habitats or find mates, but do not settle in the most densely populated areas. This indicates that natal dispersal is affected by an interplay of conspecific attraction and intraspecific competition, which has implications for population dynamics of white-tailed eagles, but also other top predators. Furthermore, our study demonstrates the value of long-term collection of both nestling and (non-invasive) adult DNA samples, and thereafter using genotype matching to identify individuals in long-lived and elusive species.

Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices.

The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.

Recombinant transmissible vaccines will be intrinsically contained despite the ability to superinfect.

INTRODUCTION: Transmissible vaccines offer a novel approach to suppressing viruses in wildlife populations, with possible applications against viruses that infect humans as zoonoses - Lassa, Ebola, rabies. To ensure safety, current designs propose a recombinant vector platform in which the vector is isolated from the target wildlife population. Because using an endemic vector creates the potential for preexisting immunity to block vaccine transmission, these designs focus on vector viruses capable of superinfection, spreading throughout the host population following vaccination of few individuals. AREAS COVERED: We present original theoretical arguments that, regardless of its R0 value, a recombinant vaccine using a superinfecting vector is not expected to expand its active infection coverage when released into a wildlife population that already carries the vector. However, if superinfection occurs at a high rate such that individuals are repeatedly infected throughout their lives, the immunity footprint in the population can be high despite a low incidence of active vaccine infections. Yet we provide reasons that the above expectation is optimistic. EXPERT OPINION: High vaccine coverage will typically require repeated releases or release into a population lacking the vector, but careful attention to vector choice and vaccine engineering should also help improve transmissible vaccine utility.

Whole genome resequencing reveals significant genetic differentiation between Exserohilum turcicum populations from maize and sorghum and candidate effector genes related to host specificity (Retracted).

After the manuscript was accepted, inconsistencies in the analyses were detected. These inconsistencies affected the general conclusion of the manuscript. This article was retracted on 27 March 2024.Exserohilum turcicum is a devastating fungal pathogen that infects both maize and sorghum, leading to severe leaf diseases of the two crops. According to host specificity, pathogenic isolates of E. turcicum are divided into two formae speciales, namely E. turcicum f. sp. zeae and E. turcicum f. sp. sorghi. To date, the molecular mechanism underlying the host specificity of E. turcicum is marginally known. In this study, the whole genomes of 60 E. turcicum isolates collected from both maize and sorghum were resequenced, which enabled identification of 147,847 high-quality SNPs in total. Based on the SNPs, all isolates were clustered into four genetic groups that had a close relationship with host source. This observation was validated by the result of principal component analysis. The analysis of population structure revealed that there was obvious genetic differentiation between maize and sorghum host populations. Further analysis showed that 5,431 SNPs, including 612 nonsynonymous SNPs, were completely co-segregated with host source. These nonsynonymous SNPs were located in 539 genes in which 18 genes were predicted to encode secretory proteins, including six putative effector genes. The sequence polymorphism analysis of the six effector genes in 60 isolates indicated that these genes were perfectly co-segregated with host source. All SNVs in the coding regions of these genes were non-synonymous substitutions, suggesting that these genes were subject to strong positive selection pressure. These findings provide new insights into the molecular basis of host specificity in E. turcicum.

New Genotypes of Phytophthora nicotianae Found on Strawberry in Florida.

Phytophthora cactorum is the most common causal agent of Phytophthora crown rot and leather rot of strawberry, but P. nicotianae is also responsible for the disease in Florida. Studies of P. nicotianae populations have suggested that different groups of genotypes are associated with different hosts; however, it is not yet clear how many lineages exist globally and how they are related to different production systems. The aim of this study was to determine the genetic relationships of P. nicotianae isolates from Florida strawberry with genotypes reported from other hosts, quantify the genetic variation on strawberry, and test for an association with nursery source. A total of 49 isolates of P. nicotianae were collected from strawberry plants originating from multiple nursery sources during six seasons of commercial fruit production in Florida. Microsatellite genotyping identified 28 multilocus genotypes on strawberry that were distinct among 208 isolates originating from various hosts and locations. Based on STRUCTURE analysis, two genetic groups were identified: one consisting of isolates from strawberry, and the other comprising samples from different hosts. Multilocus genotypes were shared among nursery sources, and populations defined by nursery were not differentiated. Both mating types were found among the isolates from North Carolina- and California-origin plants and in most strawberry seasons; however, a predominance of A1 was observed, and regular sexual reproduction was not supported by the data. This study reveals a unique genetic population of P. nicotianae associated with strawberry and emphasizes the vital role of nursery monitoring in mitigating disease spread.

Population Structure and Reproductive Biology of Monilinia vaccinii-corymbosi in Vaccinium angustifolium in Maine.

The fungus Monilinia vaccinii-corymbosi (Mvc) causes mummy berry disease in blueberries including lowbush blueberry, Vaccinium angustifolium, and is a significant pathogen of concern for Maine lowbush blueberry growers. This disease is typically managed with fungicides or by burning of plant debris containing overwintering pseudosclerotia. The population structure of Mvc in various fields in Maine was investigated using microsatellites and isolates collected from three stages in the Mvc lifecycle. The impacts of management strategies were also examined. A high level of genetic diversity was observed in Mvc from 12 lowbush blueberry fields with 199 unique multilocus haplotypes (MLHs) occurring in an original sample of 232 isolates. Twelve private alleles, including six private alleles with frequencies above 0.05, which indicated gene flow, were observed in six out of 12 fields. The population of Mvc in Maine as a whole is mostly a sexual, outcrossing population, as was seen in the diversity of MLHs and low amounts of linkage disequilibrium, although some apothecia appear to result from selfing. Three fields appear to have some clonal reproduction but were not strictly clonal, as multiple MLHs were noted in these fields. Management does not appear to affect population structure, and Mvc may be one large statewide population in Maine.

Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato.

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.

Genome-wide association study of fungicide sensitivity in a Fusarium graminearum population collected from North Dakota.

Fusarium head blight (FHB) is a destructive disease of small grains. The disease is predominantly caused by the haploid ascomycete fungus Fusarium graminearum in North America. To understand the genetics of quantitative traits for sensitivity to fungicides in this fungal pathogen, we conducted a genome-wide association study (GWAS) of sensitivity to two demethylation inhibition (DMI) class fungicides, tebuconazole and prothioconazole, using a F. graminearum population of 183 isolates collected between 1981 and 2013 from North Dakota. Baseline sensitivity to tebuconazole and prothioconazole was established using 21 isolates collected between 1981 and 1994. Most fungal isolates were sensitive to both tebuconazole and prothioconazole, however, five isolates showed significantly reduced sensitivity to prothioconazole. GWAS identified one significant marker-trait association (MTA) on chromosome 3 for tebuconazole resistance while six significant MTAs, one on chromosome 1, three on chromosome 2, and two on chromosome 4, were detected for prothioconazole resistance. Functional annotation of the MTA for tebuconazole revealed a candidate gene encoding a basic helix loop helix (bHLH) domain containing protein that reinforces sterol in the fungal membrane. Putative genes for prothioconazole resistance were also identified, which are involved in RNAi, detoxification by ubiquitin-proteasome pathway, and membrane integrity reinforcement. Considering the potential of the pathogen towards overcoming chemical control, continued monitoring of fungal sensitivities to commercially applied fungicides, especially those containing prothioconazole, is warranted to reduce risks of fungicide resistance in the pathogen populations.

Evidence of High Genetic Diversity and Differences in the Population Diversity of the Eucalyptus Leaf Blight Pathogen Calonectria pseudoreteaudii from Diseased Leaves and Soil in a Plantation in Guangxi, China.

Calonectria pseudoreteaudii is an important causal agent of Eucalyptus leaf blight in southern China. This pathogen causes Eucalyptus tree disease across numerous regions in southern China. In addition to diseased leaves, C. pseudoreteaudii has occasionally been isolated from soil in Eucalyptus plantations. The aim of this study was to clarify whether C. pseudoreteaudii causing Eucalyptus leaf blight in China is mainly clonally reproduced and to determine the potential spreading mechanism of C. pseudoreteaudii between diseased leaves and soil. To this end, 10 polymorphic microsatellite markers were analyzed to detect the genetic diversity of 97 C. pseudoreteaudii isolates from diseased leaves and soil in a Eucalyptus plantation in Guangxi Zhuang Autonomous Region, southern China. The analysis showed that the genetic diversity of the isolates from both the diseased leaves and soil was high. However, the gene and genotype diversity of the C. pseudoreteaudii isolates from diseased leaves were higher than those of the isolates from the soil. Moreover, all genotypes detected in the isolates from the soil were also found in the isolates from the diseased leaves. Structural analyses did not show clear population structures related to the population substrates of the diseased leaves or soil, and molecular variance analyses indicated that no significant genetic differentiation existed between the diseased leaf and soil populations. These results suggest that C. pseudoreteaudii in soil spreads from diseased leaves, and that an asexual cycle is the primary reproductive mode in both diseased leaf and soil populations. This is the first study on the genetic diversity and population structure of C. pseudoreteaudii. The high genetic diversity and spread pathways of this pathogen may pose challenges in controlling the disease. C. pseudoreteaudii from both diseased leaves and soils in Eucalyptus plantations needs to be carefully monitored for disease control and management.

Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Production.

Bioinformatic and experimental data show that bacteriophages are ubiquitous in human enteric microbiomes. However, there are gaps in understanding the contribution of these viruses in shaping the bacterial strain and species composition of the gut microbiome and how these phages are maintained over time. To address these questions, we adapted and analyzed the properties of a mathematical model of the population and evolutionary dynamics of bacteria and phage and performed experiments with Escherichia coli and phages isolated from four fecal microbiota transplantation (FMT) doses as representative samples of non-dysbiotic enteric microbiota. Our models predict and experiments confirm that due to production of the O antigen, E. coli in the enteric microbiome are likely to be resistant to infection with co-occurring phages. However, phages can be maintained in these populations in high densities due to high rates of transition between resistant and sensitive states, which we call leaky resistance. Based on these models and observations, we postulate that the phages found in the human gut are likely to play little role in shaping the composition of E. coli in the enteric microbiome in healthy individuals. How general this is for other species of bacteria in enteric microbiota is not yet clear, although O antigen production is broadly conserved across many taxa.